John N Nkengasong

Centers for Disease Control and Prevention, Атланта, Michigan, United States

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Publications (175)875.68 Total impact

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    ABSTRACT: Background: The Alere point-of-care (POC) Pima™ CD4 analyzer allows for decentralized testing and expansion to testing antiretroviral therapy (ART) eligibility. A consortium conducted a pooled multi-data technical performance analysis of the Pima CD4. Methods: Primary data (11,803 paired observations) comprised 22 independent studies between 2009–2012 from the Caribbean, Asia, Sub-Saharan Africa, USA and Europe, using 6 laboratory-based reference technologies. Data were analyzed as categorical (including binary) and numerical (absolute) observations using a bivariate and/or univariate random effects model when appropriate.
    BMC Medicine 07/2015; 13(1):168. DOI:10.1186/s12916-015-0396-2 · 7.28 Impact Factor
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    ABSTRACT: Mean duration of recent infection (MDRI) and misclassification of long-term HIV-1 infections, as proportion false recent (PFR), are critical parameters for laboratory-based assays for estimating HIV-1 incidence. Recent review of the data by us and others indicated that MDRI of LAg-Avidity EIA estimated previously required recalibration. We present here results of recalibration efforts using >250 seroconversion panels and multiple statistical methods to ensure accuracy and consensus. A total of 2737 longitudinal specimens collected from 259 seroconverting individuals infected with diverse HIV-1 subtypes were tested with the LAg-Avidity EIA as previously described. Data were analyzed for determination of MDRI at ODn cutoffs of 1.0 to 2.0 using 7 statistical approaches and sub-analyzed by HIV-1 subtypes. In addition, 3740 specimens from individuals with infection >1 year, including 488 from patients with AIDS, were tested for PFR at varying cutoffs. Using different statistical methods, MDRI values ranged from 88-94 days at cutoff ODn = 1.0 to 177-183 days at ODn = 2.0. The MDRI values were similar by different methods suggesting coherence of different approaches. Testing for misclassification among long-term infections indicated that overall PFRs were 0.6% to 2.5% at increasing cutoffs of 1.0 to 2.0, respectively. Balancing the need for a longer MDRI and smaller PFR (<2.0%) suggests that a cutoff ODn = 1.5, corresponding to an MDRI of 130 days should be used for cross-sectional application. The MDRI varied among subtypes from 109 days (subtype A&D) to 152 days (subtype C). Based on the new data and revised analysis, we recommend an ODn cutoff = 1.5 to classify recent and long-term infections, corresponding to an MDRI of 130 days (118-142). Determination of revised parameters for estimation of HIV-1 incidence should facilitate application of the LAg-Avidity EIA for worldwide use.
    PLoS ONE 02/2015; 10(2):e0114947. DOI:10.1371/journal.pone.0114947 · 3.23 Impact Factor
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    ABSTRACT: HIV-1 RNA viral load (VL) levels are used for monitoring disease progression and antiretroviral therapy outcomes in HIV-infected patients. To assess the performance of laboratories conducting HIV-1 VL testing in resource-limited settings, the US Centers for Disease Control and Prevention implemented a voluntary, free-of-charge, external quality assurance program using dried tube specimens (DTSs). DTS proficiency test (PT) panels consisting of 5 specimens were distributed between 2010 and 2012 at ambient temperature to participants. The results from participants (N ≥ 6) using the same assay were grouped, analyzed, and graded as acceptable within a group mean ± 3SDs. Mean proficiency scores were calculated by dividing the combined PT scores with the number of testing cycles using a linear regression model. Between 2010 and 2012, the number of participants enrolled increased from 32 in 16 countries to 114 in 44 countries. 78.2% of participants reported results using 10 different VL assays. The rates of participants reporting acceptable results were 96.6% (Abbott), 96.3% (Roche COBAS), 94.5% (Roche Amplicor), 93.0% (Biocentric), and 89.3% (NucliSENS). The overall mean proficiency scores improved over time (p = 0.024). DTSs are a good alternative specimen type to plasma specimens for VL PT programs as they do not require cold chain transportation and can be used on polymerase chain reaction (PCR)-based assays. Our data suggest that the CDC HIV-1 VL PT program using DTSs positively impacts the testing performance of the participants which might translate into better and accurate VL testing services to patients. Copyright © 2015, American Society for Microbiology. All Rights Reserved.
    Journal of Clinical Microbiology 01/2015; 53(4). DOI:10.1128/JCM.02780-14 · 4.23 Impact Factor
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    ABSTRACT: The last ten years have witnessed a significant scale-up and access to antiretroviral therapy in Africa, which has improved patient quality of life and survival. One major challenge associated with increased access to antiretroviral therapy is the development of antiretroviral resistance due to inconsistent drug supply and/or poor patient adherence. We review the current state of both acquired and transmitted drug resistance in Africa over the past ten years (2001-2011) to identify drug resistance associated with the different drug regimens used on the continent and to help guide affordable strategies for drug resistance surveillance. A total of 161 references (153 articles, six reports and two conference abstracts) were reviewed. Antiretroviral resistance data was available for 40 of 53 African countries. A total of 5,541 adult patients from 99 studies in Africa were included in this analysis. The pooled prevalence of drug resistance mutations in Africa was 10.6%, and Central Africa had the highest prevalence of 54.9%. The highest prevalence of nucleoside reverse transcriptase inhibitor mutations was in the west (55.3%) and central (54.8%) areas; nonnucleoside reverse transcriptase inhibitor mutations were highest in East Africa (57.0%) and protease inhibitors mutations highest in Southern Africa (16.3%). The major nucleoside reverse transcriptase inhibitor mutation in all four African regions was M184V. Major nonnucleoside reverse transcriptase inhibitor as well as protease inhibitor mutations varied by region. The prevalence of drug resistance has remained low in several African countries although the emergence of drug resistance mutations varied across countries. Continued surveillance of antiretroviral therapy resistance remains crucial in gauging the effectiveness of country antiretroviral therapy programs and strategizing on effective and affordable strategies for successful treatment.
    AIDS reviews 11/2014; 17(1). · 4.02 Impact Factor
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    ABSTRACT: As more HIV-infected people gain access to antiretroviral therapy (ART), monitoring HIV drug resistance (HIVDR) becomes essential to combat both acquired and transmitted HIVDR. Studies have demonstrated dried blood spots (DBS) are a suitable alternative in HIVDR monitoring using DBS collected on Whatman 903 (W-903). In this study, we sought to evaluate two other commercially available filter papers, Ahlstrom 226 (A-226) and Munktell TFN (M-TFN), for HIVDR genotyping following ambient temperature storage. DBS were prepared from remnant blood specimens collected from 334 ART patients and stored at ambient temperature for a median time of 30 days. HIV-1 viral load was determined using NucliSENS EasyQ® HIV-1 v2.0 RUO test kits prior to genotyping of the protease and reverse transcriptase regions of the HIV-1 pol gene using an in-house assay. Among the DBS tested, 26 specimens had a viral load ≥1000 copies/mL in all three types of filter paper and were included in the genotyping analysis. Genotyping efficiencies were similar between DBS collected on W-903 (92.3%), A-226 (88.5%), and M-TFN (92.3%) filter papers (P = 1.00). We identified 50 DR-associated mutations in DBS collected on W-903, 33 in DBS collected on A-226, and 48 in DBS collected on M-TFN, resulting in mutation detection sensitivities of 66.0% for A-226 and 88.0% for M-TFN when compared to W-903. Our data indicate that differences among filter papers may exist at this storage condition and warrant further studies evaluating filter paper type for HIVDR monitoring.
    PLoS ONE 10/2014; 9(10):e109060. DOI:10.1371/journal.pone.0109060 · 3.23 Impact Factor
  • Elizabeth T Luman · Katy Yao · John Nkengasong
    09/2014; 3(2). DOI:10.4102/ajlm.v3i2.265
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    ABSTRACT: Fourth-generation HIV rapid tests (RTs) claim to detect both p24 antigen (Ag) and HIV antibodies (Ab) for early identification of acute infections, important for targeted prevention and reducing HIV transmission. In a nationally representative household survey in Swaziland, 18,172 adults, age 18-49 years, received home-based HIV rapid testing in 2010-2011. Of the 18,172 individuals, 5,822 (32.0%) were Ab+ by Determine HIV-1/2 Ab/Ab Combo and of those, 5,789 (99.4%) were confirmed reactive by Uni-Gold. Determine Combo identified 12 individuals as acute infections (Ag+/Ab-); however, none had detectable HIV-1 RNA and 8 of 12 remained HIV negative at 6-week follow-up visits (4 lost to follow up). All RT non-reactive samples were pooled and tested by nucleic acid amplification testing (NAAT) to identify acute infections. NAAT identified 13 (0.1%) of the 12,338 HIV antibody-negative specimens as HIV RNA positive with RNA levels ranging from 300 to >10,000,000 copies/mL. However, none of them were Ag+ on Determine Combo. Follow-up testing of 12 of the 13 NAAT-positive individuals at 6 months demonstrated 12 seroconversions (1 lost to follow-up). Therefore, the Combo test had a sensitivity of 0% (95% CI 0%-28%) and positive predictive value of 0% for the detection of acute infections. The ability of Determine 4(th) Generation Combo to detect antigen was very poor in Swaziland. Thus, Determine Combo does not add any value to the current testing algorithm; rather it adds additional costs and complexity to HIV diagnosis. The detection of acute HIV infections may need to rely on other testing strategies.
    Journal of Clinical Microbiology 08/2014; 52(10). DOI:10.1128/JCM.01989-14 · 4.23 Impact Factor
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    ABSTRACT: Abstract Strong laboratory services and systems are critical for delivering timely and quality health services that are vital to reduce patient attrition in the HIV treatment and prevention cascade. However, challenges exist in ensuring effective laboratory health systems strengthening and linkages. In particular, linkages and referrals between laboratory testing and other services need to be considered in the context of an integrated health system that includes prevention, treatment, and strategic information. Key components of laboratory health systems that are essential for effective linkages include an adequate workforce, appropriate point-of-care (POC) technology, available financing, supply chain management systems, and quality systems improvement, including accreditation. In this review, we highlight weaknesses of and gaps between laboratory testing and other program services. We propose a model for strengthening these systems to ensure effective linkages of laboratory services for improved access and retention in care of HIV/AIDS patients, particularly in low- and middle-income countries.
    AIDS patient care and STDs 04/2014; DOI:10.1089/apc.2013.0356 · 3.58 Impact Factor
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    ABSTRACT: A voluntary, cost-free external quality assessment (EQA) program established by the U.S. Centers for Disease Control and Prevention (CDC) was implemented to primarily monitor the performance of laboratories conducting HIV Early Infant Diagnosis (EID) from dried blood spots (DBS) in low to middle-income countries since 2006. Ten blinded DBS proficiency test (PT) specimens and 100 known HIV-positive and negative DBS specimens (to be used as internal controls) were shipped tri-annually to participating laboratories with reports for the PT specimens due within 30 days. The participant's results and summary of the performance of all participating laboratories and each diagnostic method were provided after each test cycle. Enrollment in the CDC PT program expanded progressively from 17 laboratories from 11 countries in 2006 to include 136 laboratories from 41 countries at the end of 2012. Despite external pressures to test and treat more children while expanding EID programs, mean PT test scores significantly improved over time as demonstrated by the upward trend from mid-2006 to end of 2012 (P = 0.001) and increase in the percentage of laboratories scoring 100% (P =0.003). The mean test scores plateaued over the past 10 testing cycles, ranging between 98.2 and 99.7% and discordant test results still occur, but at a rate no higher than 2.6%. Analysis of these test results suggests a positive impact of proficiency testing on the testing performance of the participating laboratories and a continuous training program and proficiency testing participation may translate into laboratories improving their testing accuracy.
    Journal of clinical microbiology 12/2013; 52(3). DOI:10.1128/JCM.03097-13 · 4.23 Impact Factor
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    ABSTRACT: Detection of recent HIV infections is a prerequisite for reliable estimations of transmitted HIV drug resistance (t-HIVDR) and incidence. However, accurately identifying recent HIV infection is challenging due partially to the limitations of current serological tests. Ambiguous nucleotides are newly emerged mutations in quasispecies, and accumulate by time of viral infection. We utilized ambiguous mutations to establish a measurement for detecting recent HIV infection and monitoring early HIVDR development. Ambiguous nucleotides were extracted from HIV-1 pol-gene sequences in the datasets of recent (HIVDR threshold surveys [HIVDR-TS] in 7 countries; n=416) and established infections (1 HIVDR monitoring survey at baseline; n=271). An ambiguous mutation index of 2.04×10(-3) nts/site was detected in HIV-1 recent infections which is equivalent to the HIV-1 substitution rate (2×10(-3) nts/site/year) reported before. However, significantly higher index (14.41×10(-3) nts/site) was revealed with established infections. Using this substitution rate, 75.2% subjects in HIVDR-TS with the exception of the Vietnam dataset and 3.3% those in HIVDR-baseline were classified as recent infection within one year. We also calculated mutation scores at amino acid level at HIVDR sites based on ambiguous or fitted mutations. The overall mutation scores caused by ambiguous mutations increased (0.54×10(-2)3.48×10(-2)/DR-site) whereas those caused by fitted mutations remained stable (7.50-7.89×10(-2)/DR-site) in both recent and established infections, indicating that t-HIVDR exists in drug-naïve populations regardless of infection status in which new HIVDR continues to emerge. Our findings suggest that characterization of ambiguous mutations in HIV may serve as an additional tool to differentiate recent from established infections and to monitor HIVDR emergence.
    PLoS ONE 10/2013; 8(10):e77649. DOI:10.1371/journal.pone.0077649 · 3.23 Impact Factor
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    ABSTRACT: High-throughput, sensitive and cost-effective HIV drug resistance (HIVDR) detection assays are needed for large-scale monitoring of the emergence and transmission of HIVDR in resource-limited settings. Using suspension array technology, we have developed a multiplex allele-specific (MAS) assay that can simultaneously detect major HIVDR mutations at 20 loci. Forty-five allele-specific primers tagged with unique 24-base oligonucleotide at the 5' end were designed to detect wild-type and mutant alleles at the 20 loci of HIV-1 subtype-C viruses. The MAS assay was first established and optimized with three plasmid templates (C-wt, C-mut1 and C-mut2), and then evaluated using 148 plasma specimens from HIV-1 subtype-C-infected individuals. All the wild-type and mutant alleles could be unequivocally distinguished with plasmid templates, and the limits of detection were 1.56% for K219Q and K219E; 3.13% for L76V; 6.25% for K65R, K70R, L74V, L100I, K103N, K103R, Q151M, Y181C and I47V; and 12.5% for M41L, K101P, K101E, V106A, V106M, Y115F, M184V, Y188L, G190A, V32I, I47A, I84V and L90M. Analyses of 148 plasma specimens revealed that MAS assay gave 100% concordance with conventional sequencing at eight loci, and over 95% (95.21%-99.32%) concordance at the remaining 12 loci. The differences observed were mainly caused by 24 additional low-abundance alleles detected by the MAS assay. Ultra-deep sequencing analysis confirmed 15 of 16 low-abundance alleles. The multiplex, sensitive and straightforward result reporting assay represents a new efficient genotyping tool for HIVDR surveillance and monitoring.
    Journal of clinical microbiology 08/2013; 51(11). DOI:10.1128/JCM.01669-13 · 4.23 Impact Factor
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    ABSTRACT: Abstract Whatman 903 filter paper is the only filter paper that has been used for HIV drug resistance (HIVDR) genotyping in resource-limited settings. In this study, we evaluated another dried blood specimen collection device, termed SampleTanker(®) (ST), for HIVDR genotyping. Blood specimens from 123 antiretroviral therapy (ART)-experienced patients were used to prepare ST whole blood and ST plasma specimens; they were then stored at ambient temperature for 2 or 4 weeks. The remaining plasma specimens were stored at -80°C and used as frozen plasma controls. Frozen plasma viral load (VL) was determined using the Roche Amplicor HIV-1 Monitor test, v.1.5 and 50 specimens with VL ≥3.00 log10 copies/ml were genotyped using the broadly sensitive genotyping assay. The medium VL for the 50 frozen plasma specimens with VL ≥3.00 log10 was 3.58 log10 copies/ml (IQR: 3.32-4.11) and 96.0% (48/50) of them were genotyped. Comparing to frozen plasma specimens, significantly lower genotyping rates were obtained from ST whole blood (48.98% and 42.85%) and ST plasma specimens (36.0% and 36.0%) stored at ambient temperature for 2 and 4 weeks, respectively (p<0.001). Nucleotide sequence identity and resistance profile analyses between the matched frozen plasma and ST whole blood or ST plasma specimens revealed high nucleotide sequence identities and concordant resistance profiles (98.1% and 99.0%, and 96.6% and 98.9%, respectively). Our results indicate that with the current design, the ST may not be the ideal dried blood specimen collection device for HIVDR monitoring for ART patients in resource-limited settings.
    AIDS research and human retroviruses 08/2013; 30(1). DOI:10.1089/aid.2013.0127 · 2.46 Impact Factor
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    ABSTRACT: Laboratory systems worldwide are challenged not only by the need to compete for scarce resources with other sections of national health care programmes, but also with the lack of understanding of the critical role that laboratories play in the accurate diagnosis and monitoring of patients suffering from high-burdens of disease. An effective approach to establishing cost-effective laboratory systems that provide rapid and accurate test results for optimal impact on patient care is to move away from disease-specific programmes and establish integrated laboratory services. An integrated laboratory network provides all primary diagnostic services needed for care and treatment without requiring patients to go to different laboratory facilities for specific tests. Such a network focuses on providing quality-assured basic laboratory testing through the use of common specimen collection, reporting and diagnostic platforms that can be used across diseases. An integrated laboratory system also provides specimen transport to specialised laboratories and an environment conducive to the introduction and use of new and more complex technologies that would benefit the patient population and public health systems as a whole. As such, this article described various strategies for, and practical examples of, the successful integration of laboratory services.
    04/2013; DOI:10.4102/ajlm.v1i1.11
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    ABSTRACT: In Kenya, HIV-1 viral load monitoring is commonly performed with the Cobas Amplicor using plasma specimens. Interest is growing in transitioning to real-time PCR (RT-PCR), such as the Cobas Ampliprep/Cobas TaqMan (CAP/CTM), using dried blood spots (DBS). Before implementation, direct evaluation of the two assays using DBS field specimens is required. This study compares the sensitivity, specificity, negative and positive predictive values (NPV and PPV, respectively), concordance, and agreement between HIV-1 viral load measurements using plasma and DBS specimens obtained from 512 HIV-1-infected pregnant females enrolled in the Kisumu Breastfeeding Study and tested with the Cobas Amplicor and CAP/CTM assays. The sensitivity and NPV of viral load detection in DBS specimens were higher with CAP/CTM (sensitivity, 100%; 95% confidence interval [CI], 99.1 to 100.0%; NPV, 100%; 95% CI, 59.0 to 100.0%) than the Cobas Amplicor (sensitivity, 96.6%; 95% CI, 94.3 to 98.1%; NPV, 58.8%; 95% CI, 40.7 to 75.4%). The PPVs were comparable between both assays when using DBS. The specificity of viral load detection in DBS specimens was lower with CAP/CTM (77.8%; 95% CI, 40.0 to 97.2%) than that of the Cobas Amplicor (95.2%; 95% CI, 76.2 to 99.9%). Good concordance and agreement were observed when paired plasma and DBS specimens were tested with both assays. Lower specificity with the CAP/CTM is likely due to proviral HIV-1 DNA amplification and lower detection limits with RT-PCR. However, the CAP/CTM has better sensitivity and higher throughput than the Cobas Amplicor. These findings suggest that DBS may be a suitable alternative to plasma when using RT-PCR, which could increase access to viral load monitoring in resource-limited settings.
    Journal of clinical microbiology 04/2013; 6(51):1208-18. · 4.23 Impact Factor
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    ABSTRACT: In Kenya, HIV-1 viral load monitoring is commonly performed with the Cobas Amplicor using plasma specimens. Interest is growing in transitioning to real-time PCR (RT-PCR), such as the Cobas Ampliprep/Cobas TaqMan (CAP/CTM), using dried blood spots (DBS). Before implementation, direct evaluation of the two assays using DBS field specimens is required. This study compares the sensitivity, specificity, negative and positive predictive values (NPV and PPV, respectively), concordance, and agreement between HIV-1 viral load measurements using plasma and DBS specimens obtained from 512 HIV-1-infected pregnant females enrolled in the Kisumu Breastfeeding Study and tested with the Cobas Amplicor and CAP/CTM assays. The sensitivity and NPV of viral load detection in DBS specimens were higher with CAP/CTM (sensitivity, 100%; 95% confidence interval [CI], 99.1 to 100.0%; NPV, 100%; 95% CI, 59.0 to 100.0%) than the Cobas Amplicor (sensitivity, 96.6%; 95% CI, 94.3 to 98.1%; NPV, 58.8%; 95% CI, 40.7 to 75.4%). The PPVs were comparable between both assays when using DBS. The specificity of viral load detection in DBS specimens was lower with CAP/CTM (77.8%; 95% CI, 40.0 to 97.2%) than that of the Cobas Amplicor (95.2%; 95% CI, 76.2 to 99.9%). Good concordance and agreement were observed when paired plasma and DBS specimens were tested with both assays. Lower specificity with the CAP/CTM is likely due to proviral HIV-1 DNA amplification and lower detection limits with RT-PCR. However, the CAP/CTM has better sensitivity and higher throughput than the Cobas Amplicor. These findings suggest that DBS may be a suitable alternative to plasma when using RT-PCR, which could increase access to viral load monitoring in resource-limited settings.
    Journal of Clinical Microbiology 04/2013; 51(4). DOI:10.1128/JCM.03048-12 · 4.23 Impact Factor
  • 03/2013; 2(1). DOI:10.4102/ajlm.v2i1.31
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    ABSTRACT: In Kenya, HIV-1 viral load monitoring is commonly performed with the COBAS Amplicor using plasma specimens. Interest is growing in transitioning to real-time PCR (RT-PCR), such as the COBAS Ampliprep/COBAS Taqman (CAP/CTM), using dried blood spots (DBS). Before implementation, direct evaluation of the two assays using DBS field specimens is required. This study compares sensitivity, specificity, negative (NPV) and positive (PPV) predictive values, concordance, and agreement between HIV-1 viral load measurements using plasma and DBS specimens obtained from 512 HIV-1 infected pregnant females enrolled in the Kisumu Breastfeeding Study, and tested with the COBAS Amplicor and CAP/CTM assays. The sensitivity and NPV of viral load detection in DBS specimens were higher with CAP/CTM (sensitivity: 100%, 95% CI: 99.1-100.0; NPV: 100%, 95% CI: 59.0-100.0%) than the COBAS Amplicor (sensitivity: 96.6%, 95% CI: 94.3-98.1; NPV: 58.8%, 95% CI: 40.7-75.4). PPV was comparable between both assays when using DBS. The specificity of viral load detection in DBS specimens was lower with CAP/CTM (77.8%, 95% CI: 40.0-97.2) than the COBAS Amplicor (95.2%, 95% CI: 76.2-99.9). Good concordance and agreement were observed when testing paired plasma and DBS specimens with both assays. Lower specificity with the CAP/CTM is likely due to pro-viral HIV-1 DNA amplification and lower detection limits with RT-PCR. However, the CAP/CTM has better sensitivity and higher throughput when compared with the COBAS Amplicor. These findings suggest that DBS may be a suitable alternative to plasma when using RT-PCR, which could increase access to viral load monitoring in resource limited settings.
    Journal of clinical microbiology 02/2013; · 4.23 Impact Factor
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    ABSTRACT: Participation in external quality assessment programs is critical to ensure quality clinical laboratory testing. Commercially available proficiency test panels for HIV-1 virus load testing that are used commonly in external quality assessment programs remain a financial obstacle to resource-limited countries. Maintaining cold-chain transportation largely contributes to the cost of traditional liquid proficiency test panels. Therefore, we developed and evaluated a proficiency test panel using dried tube specimens that can be shipped and stored at ambient temperature. This dried tube specimens panel consisted of 20μl aliquots of a HIV-1 stock that were added to 2ml tubes and left uncapped for drying, as a preservation method. The stability of dried tube specimens at concentrations ranging from 10(2) to 10(6.5) RNA copies/ml was tested at different temperatures over time, showing no viral load reduction at 37°C and a decrease in viral load smaller than 0.5 Log(10) at 45°C for up to eight weeks when compared to initial results. Eight cycles of freezing-thawing had no effect on the stability of the dried tube specimens. Comparable viral load results were observed when dried tube specimen panels were tested on Roche CAPTAQ, Abbott m2000, and Biomerieux easyMAG viral load systems. Preliminary test results of dried proficiency test panels shipped to four African countries at ambient temperature demonstrated a low inter assay variation (SD range: 0.29-0.41 Log(10) RNA copies/ml). These results indicated that HIV-1 proficiency test panels generated by this methodology might be an acceptable alternative for laboratories in resource-limited countries to participate in external quality assessment programs.
    Journal of virological methods 12/2012; 188(1-2). DOI:10.1016/j.jviromet.2012.11.036 · 1.88 Impact Factor
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    ABSTRACT: HIV-1 drug resistance (HIVDR) assays are important tools in clinical management of HIV-infected patients on antiretroviral therapy (ART) and surveillance of drug resistant variants at population levels. The high cost associated with commercial assays hinders their use in resource-limited settings. We adopted and validated a low cost in-house assay using 68 matched plasma and dried blood spot (DBS) samples with a median viral load (VL) of 58,187copies/ml, ranging from 253 to 3,264,850 against the commercial assay ViroSeq. Results indicated that the in-house assay not only had higher plasma genotyping rate than ViroSeq (94% vs. 78%), but also was able to genotype 89.5% (51/57) of the matched DBS samples with VLs of ≥1,000 copies/ml. The sensitivity in detecting DR mutations by the in-house assay was 98.29% (95% CI: 97.86-98.72) on plasma and 96.54 (95% CI: 95.93-97.15) on DBS and the specificity was 99.97% (95% CI: 99.91-100.00) for both sample types when compared to ViroSeq. The minor DR mutation differences detected by the in-house assay against the Viroseq didn't result in the clinical significance. In addition, cost analysis showed that the in-house assay could reduce the genotyping cost by about 60% for both plasma and DBS comparing to ViroSeq.This field condition evaluation highlights the potential utility of a cost-effective, subtype-independent in-house genotyping assay using both plasma and DBS specimens for HIVDR clinical monitoring and population based surveillance in resource-limited settings.
    Journal of clinical microbiology 12/2012; 51(2). DOI:10.1128/JCM.02347-12 · 4.23 Impact Factor

Publication Stats

4k Citations
875.68 Total Impact Points

Institutions

  • 2001–2015
    • Centers for Disease Control and Prevention
      • • Division of Global HIV/AIDS
      • • National Center for HIV/AIDS, Viral Hepatitis, STD and TB Prevention
      • • Division of HIV/AIDS Prevention, Intervention and Support
      • • National Center for Emerging and Zoonotic Infectious Diseases
      Атланта, Michigan, United States
    • Uganda Virus Research Institute
      Entebbe, Central Region, Uganda
  • 2013
    • Kenya Medical Research Institute
      • Centre for Global Health Research
      Nairobi, Nairobi Province, Kenya
  • 2004
    • National Institute of Allergy and Infectious Diseases
      Maryland, United States
  • 1992–2003
    • Institute Of Tropical Medicine
      Antwerpen, Flemish, Belgium
  • 2001–2002
    • Institut de Recherches Mathematiques , Cote d'Ivoire, Abidjan
      Abijan, Lagunes, Ivory Coast
  • 1998–2000
    • Kenya Centers for Disease Control and Prevention
      Winam, Kisumu, Kenya
    • Los Alamos National Laboratory
      Лос-Аламос, California, United States
    • University of Tours
      Tours, Centre, France
  • 1994–1999
    • University of Yaoundé II
      Jaúnde, Centre, Cameroon
  • 1995
    • Max von Pettenkofer-Institut
      München, Bavaria, Germany